[Bioc-devel] Git Transition Plan

On 03/29/2017 03:55 PM, Henrik Bengtsson wrote:

Thanks.  I have a few thoughts and questions in order to plan ahead:

- Our plan is to make a 'clean' transition from SVN to git, 
approximately one month after the next Bioconductor release. 
Developers or users will not have access to the SVN system after the 
date of transition.

In order to preserve commit authorship, what's your plan for mapping
SVN username to Git 'user.email' and 'user.name'?  The 'user.email' is
what GitHub uses to associate commits and contributions to GitHub
accounts.

The svn administrators kept a comprehensive (but not complete) record 
of svn id, real user name, and contact email at the time the svn id 
was create. We use this to map between svn commits and git user name 
and email address.

The information is not entirely consistent, with some fields for some 
records 'missing' (e.g., my record doesn't contain my real name) and 
of course out of date (e.g., my email address).

Our intention is NOT to re-write history, but to map the information 
that we have to the git repositories. So my svn commits appear without 
a proper name, and with an outdated email address. Of course, new 
commits after the transition will contain whatever info git provides.

BTW, using obsolete email addresses may prevent people from being
associated with those email addresses on GitHub and other online
services that require authentication of authorship claims (which go
out via those email addresses).

When I SVN-to-Git exported my Bioconductor packages a few years ago, I
could handle manually because there were not too many contributors in
the SVN logs and I reached out to each of them and asked what email
addresses they would prefer to have in the Git commits.  That approach
is obviously not feasible to automate for all Bioconductor packages.
Maybe this can be handled optionally by each package maintainers by
adding a .gitauthors file to the package root (or possibly via a
global Bioc one that everyone can commit to), e.g.
```r
hb = Henrik Bengtsson <henrikb at braju.com>
joe at foo.com = John Doe <jd at someone.org>
```
and then Bioc can use this mapping when exporting to Git?

Finally, will people like me who already done the SVN-to-Git migration
be able to use that instead of the Bioc generated one? (I assume not,
but worth asking)

No, we'll make a git snapshots of svn at the time of transition, and 
these git repositories will be the cannonical version -- developers 
will need to sync with these as they see fit.

Martin

Thanks,

Henrik

On Wed, Mar 29, 2017 at 9:51 AM, Turaga, Nitesh
<Nitesh.Turaga at roswellpark.org> wrote:

Dear Bioconductor Developers,

More news about the Git transition plan. We are coming close to our 
transition date and have made significant progress in getting our 
new server ready for the Bioconductor community.

1. Overall plan:

- Bioconductor hosts each package as a distinct repository at 
git.bioconductor.org<http://git.bioconductor.org/>. From 
Bioconductor's perspective, this is the canonical location. Nightly 
builds will be based on these repositories, release branches will be 
created in these repositories, etc. The naming convention for 
branches remains the same.

- Developers clone or otherwise sync their code base to these 
repositories. Each developer will be able to push to and pull from 
(e.g., during branching and version bumps at package release) their 
git.bioconductor.org<http://git.bioconductor.org/> repository. 
Version bumps and new branches(during Bioconductor release) will be 
handled by the core team.

- Developers are encouraged to host and develop their source code on 
Github or other git-based social platforms. This promotes community 
involvement, and empowers developers to adopt best practices related 
to issue tracking, continuous integration, bug fixes, pull requests 
from their community, etc.

- All bioconductor infrastructure code will also be available on 
Github, through our organization 
page(https://github.com/Bioconductor). Community members are 
encouraged to send us pull requests for all our public repositories.

2. Timing:

- Our plan is to make a 'clean' transition from SVN to git, 
approximately one month after the next Bioconductor release. 
Developers or users will not have access to the SVN system after the 
date of transition.

3. Repositories:

- The git repositories will be derived from a 'snapshot' of the 
latest SVN repository at the time of the transition. After the date 
of transition, further commits to SVN will not be reflected in the 
new git repositories.

- Each repository will capture the full SVN commit history of the 
package. Releases will be included as branches in the repository.

- We anticipate that software and experiment data packages will be 
hosted at git.bioconductor.org<http://git.bioconductor.org/>. 
Experiment data packages will use git-lfs to manage large data.

- The Github Bioconductor-mirror repository will be removed.

4. Test phases:

- We anticipate two test periods.

- A private 'alpha' test phase is starting shortly. Alpha testers 
will initially have pull access to their repository, and will follow 
tentative work flows for gaining push access, for maintaining clones 
of their packages, for committing to the 
git.bioconductor.org<http://git.bioconductor.org/> repositories, and 
for pulling from (e.g., version bumps and release branches) the 
repositories.

- A public 'beta' test phase will start after the next Bioconductor 
release, and last for approximately four weeks. Beta testers will 
have pull access to all Bioconductor package repositories, and push 
access to packages that they maintain. Commits will be visible, but 
NOT synced with SVN or incorporated into nightly builds.

- An essential activity during test periods is to verify that the 
SVN commit history has been captured in the git repositories. This 
will be available in your git log.

5. Resources:

- We will be developing resources to help developers in the transition.

- As an addition to the resources, we also recommend the excellent 
tutorials provided at 
gittutorial<https://git-scm.com/docs/gittutorial>, 
try.github.io<https://try.github.io/>.

Best,

Nitesh Turaga
Bioconductor Core Team


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